BMB Reports

Korean Society for Biochemistry and Molecular Biology (생화학분자생물학회)
권호 표지
DOI QR코드

DOI QR Code

Compositional Correlations in Canine Genome Reflects Similarity with Human Genes

  • Joy, Faustin (Department of Animal Genetics and Breeding, West Bengal University of Animal & Fishery Sciences) ;
  • Basak, Surajit (Bioinformatics Centre, Bose Institute) ;
  • Gupta, Sanjib Kumar (Bioinformatics Centre, Bose Institute) ;
  • Das, Pranab Jyoti (Department of Animal Genetics and Breeding, West Bengal University of Animal & Fishery Sciences) ;
  • Ghosh, Shankar Kumar (Department of Animal Genetics and Breeding, West Bengal University of Animal & Fishery Sciences) ;
  • Ghosh, Tapash Chandra (Bioinformatics Centre, Bose Institute)
  • Received : 2005.05.28
  • Accepted : 2006.01.17
  • Published : 2006.05.31
Download PDF
⟨ Previous Next ⟩

Abstract

The base compositional correlations that hold among various coding and noncoding regions of the canine genome have been analysed. The distribution pattern of genes, on the basis of $GC_3$ composition, shows a wide range similar to that observed in human. However the occurrence of maximum number of genes was observed in the range of 65-75% of $GC_3$ composition. The correlation between the coding DNA sequences of canine with the different noncoding regions (introns and flanking regions) is found to be significant and in many cases the degree of correlation show similarity to human genome. We found that these correlations are not limited to the GC content alone, but is holding at the level of the frequency of individual bases as well. The present study suggests that canines ideally belong to the predicted 'general mammalian pattern' of genome composition along with human beings.

Keywords

References

  1. Banerjee, T., Gupta, S. K. and Ghosh, T. C. (2005) Compositional transitions between Oryza sativa and Arabidopsis thaliana genes are linked to the functional change of encoded proteins. Plant Science 170, 267-273 https://doi.org/10.1016/j.plantsci.2005.08.012
  2. Bernardi, G., Olofsson, B., Filipski, J., Zerial, M., Salinas, J., Cuny, G., Meunier-Rotival, M. and Rodier, F. (1985) The mosaic genome of warm-blooded vertebrates. Science 228, 953-958 https://doi.org/10.1126/science.4001930
  3. Bernardi, G. (1991) The distribution of genes in the human genome. Gene 100, 181-187 https://doi.org/10.1016/0378-1119(91)90364-H
  4. Bernardi, G. (2004) Structural and Evolutionary Genomics: Natural Selection in Genome Evolution, Elsevier, Amsterdam, USA
  5. Chase, K., Carrier, D. R., Adler, F. R., Jarvik, T., Ostrander, E. A., Lorentzen, T. D. and Lark, K. G. (2002) Genetic basis for systems of skeltal quantitative traits: principal component analysis of canid skelton. Proc. Natl. Acad. Sci. USA 99, 9930- 9935 https://doi.org/10.1073/pnas.152333099
  6. Clay, O., Caccio, S., Zoubak, S., Mouchiroud, D. and Bernardi, G. (1996) Human coding and noncoding DNA: compositional correlations. Mol. Phylogenet. Evol. 5, 2-12. https://doi.org/10.1006/mpev.1996.0002
  7. D'Onofrio, G., Mouchiroud, D., Aissani, B., Gautier, C. and Bernardi, G. (1991) Correlations between the compositional properties of human genes, codon usage and amino acid composition of proteins. J. Mol. Evol. 32, 504-510 https://doi.org/10.1007/BF02102652
  8. D'Onofrio, G., Jabbari, K., Musto, H. and Bernardi, G. (1999) The correlations of protein hydropathy with the composition of coding sequences. Gene 238, 3-14 https://doi.org/10.1016/S0378-1119(99)00257-7
  9. Federico, C., Saccone, S., Andreozzi, L., Motta, S., Russo, V., Carels, N. and Bernardi, G. (2004) The pig genome: compositional analysis and identification of the gene richest regions in chromosomes and nuclei. Gene 343, 245-251 https://doi.org/10.1016/j.gene.2004.09.011
  10. Greer, K. A., Corgill, E. J., Cox, M. L., Clark, L. A., Tsai, K. L., Credille, K. M., Dunstan, R. W., Venta, P. J. and Murphy, K. E. (2003) Digging up the canine genome - a tale to wag about. Cytogenet. Genome Res. 102, 244-248 https://doi.org/10.1159/000075756
  11. Gupta, S. K., Bhattacharya, T. K. and Ghosh, T. C. (2004) Synonymous codon usage in Lactococcus lactis: mutational bias versus translational selection. J. Biomol. Struct. Dyn. 21, 1-9.
  12. Jabbari, K. and Bernardi, G. (2000) The distribution of genes in the Drosophila genome. Gene 247, 287-292 https://doi.org/10.1016/S0378-1119(00)00128-1
  13. Kirkness, E. F., Batna, V., Halpern, A. L., Levy, S., Remington, K., Rusch, D. B., Delcher, A. L., Pop, M., Wang, W., Fraser, C. M. and Venter, J. C. (2003) The dog genome: survey sequencing and comparative analysis. Science 301, 1898-1903 https://doi.org/10.1126/science.1086432
  14. Mouchiroud, D., D'Onofrio, G., Aissani, B., Macaya, G., Gautier, C. and Bernardi, G. (1991) The distribution of genes in the human genome. Gene 100, 181-187 https://doi.org/10.1016/0378-1119(91)90364-H
  15. Musto, H., Romero, H., Zavala, A. and Bernardi, G. (1999) Compositional correlations in the chicken genome. J. Mol. Evol. 49, 325-329 https://doi.org/10.1007/PL00006555
  16. Ostrander, E. A., Galibert, F. and Patterson, D. F. (2000) Canine genetics comes of age. Trends Genet. 16, 117-124 https://doi.org/10.1016/S0168-9525(99)01958-7
  17. Patterson, D. F. (2000) Canine genetic information system: a compositional knowledge base of genetic diseases in the dog. Mosby-Harcourt, St Louis, USA

Cited by

  1. Immunopathogenic behaviors of canine transmissible venereal tumor in dogs following an immunotherapy using dendritic/tumor cell hybrid vol.139, pp.2-4, 2011, https://doi.org/10.1016/j.vetimm.2010.10.013
  2. Composition Profile of the Human Genome at the Chromosome Level vol.27, pp.3, 2009, https://doi.org/10.1080/07391102.2009.10507322
  3. Pharmacogenetic and Metabolic Differences Between Dog Breeds: Their Impact on Canine Medicine and the Use of the Dog as a Preclinical Animal Model vol.10, pp.1, 2008, https://doi.org/10.1208/s12248-008-9011-1
  4. Comparative oncology: ErbB-1 and ErbB-2 homologues in canine cancer are susceptible to cetuximab and trastuzumab targeting vol.50, pp.4, 2012, https://doi.org/10.1016/j.molimm.2012.01.002
  5. A Role for T-Lymphocytes in Human Breast Cancer and in Canine Mammary Tumors vol.2014, 2014, https://doi.org/10.1155/2014/130894
  6. Transmission and expansion of HOXB4-induced leukemia in two immunosuppressed dogs: Implications for a new canine leukemia model vol.37, pp.10, 2009, https://doi.org/10.1016/j.exphem.2009.07.004